Variant report

Variant	rs6531212
Chromosome Location	chr2:20338020-20338021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20333298..20335083-chr2:20336801..20339415,3	MCF-7	breast:
2	chr2:20335576..20338444-chr2:20340414..20343314,2	MCF-7	breast:
3	chr2:20331753..20338544-chr2:20423396..20426851,7	MCF-7	breast:
4	chr2:20337846..20345492-chr2:20421951..20427912,20	MCF-7	breast:
5	chr2:20329032..20331915-chr2:20335666..20338081,2	K562	blood:
6	chr2:20337265..20341089-chr2:20350774..20352905,3	MCF-7	breast:
7	chr2:20337444..20339646-chr2:20346771..20348752,3	K562	blood:
8	chr2:20337943..20339781-chr2:20440537..20442934,2	MCF-7	breast:
9	chr2:20337465..20342202-chr2:20382545..20388364,6	MCF-7	breast:
10	chr2:20302794..20305910-chr2:20337863..20340597,3	MCF-7	breast:
11	chr2:20336087..20338079-chr2:20398729..20401526,2	MCF-7	breast:
12	chr2:20335603..20338539-chr2:20339889..20342133,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction
ENSG00000235411	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10185277	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691940	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348314	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34277789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666364	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666365	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666366	0.80[GIH][hapmap]
rs6744463	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6531212	CPSF3	trans	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20331800-20338600	Weak transcription	Small Intestine	intestine
2	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:20334200-20346600	Enhancers	Placenta	Placenta
4	chr2:20335400-20339800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:20335600-20339200	Enhancers	K562	blood
6	chr2:20335800-20343400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:20336000-20338400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:20336000-20338600	Weak transcription	A549	lung
9	chr2:20336000-20338800	Weak transcription	Fetal Intestine Small	intestine
10	chr2:20336000-20339200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:20336000-20340600	Weak transcription	Liver	Liver
12	chr2:20336200-20338800	Weak transcription	Esophagus	oesophagus
13	chr2:20336200-20338800	Weak transcription	Stomach Mucosa	stomach
14	chr2:20336200-20339400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:20336400-20338600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:20336400-20339200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:20336400-20346200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:20336800-20340200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:20336800-20341800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:20337000-20338200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:20337000-20338600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:20337000-20338800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:20337200-20338200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:20337200-20340000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:20337200-20340600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:20337400-20338600	Weak transcription	Fetal Lung	lung
27	chr2:20337400-20338800	Weak transcription	Spleen	Spleen
28	chr2:20337400-20340000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:20337400-20343400	Enhancers	NHEK	skin
30	chr2:20337600-20338800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:20337600-20339200	Weak transcription	Colonic Mucosa	Colon
32	chr2:20337800-20338600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:20337800-20340200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:20337800-20341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:20338000-20339000	Enhancers	Fetal Kidney	kidney
36	chr2:20338000-20339800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:20338000-20340000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr2:20338000-20340800	Enhancers	Hela-S3	cervix
39	chr2:20338000-20345200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:20338000-20346800	Enhancers	HMEC	breast

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